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"imageNCIF" workshop
- Subject: "imageNCIF" workshop
- From: Andy Hammersley <hammersl@esrf.fr>
- Date: Thu, 28 Aug 97 13:59:16 +0200
Hello Everybody, I've just joined the group so I'll start by briefly introducing myself. I'm Andy Hammersley (hammersley@esrf.fr) and I work at the European Synchrotron Radiation Facility in Grenoble, as a scientific programmer. I'm the author of the FIT2D data analysis program, which some of you may know. My work covers many areas of X-ray science, including support for SAS experiments. Frustration with the multitude of image data formats which keep being invented (sometimes poorly), has led me to get involved with a project to define an international data format for image storage within the "crystallographic" community. ("Crystallographic" should be interpreted in a very wide sense; e.g. the IUCr includes the SAS commission.) This is being done in accord with the IUCr COMCIFS committee with the aim of IUCr recognition, and hopefully widespread acceptence. John Barnes suggested that I post information on this initiative to the SAS community. At the end of this message is an article (very slightly adapted) which I originally wrote for the CCP-13 newsletter. There is also the reference for the paper which describes the CIF format and the original "data dictionary". Much e-mail discussion has already taken place concerning the format, but to bring ideas clearly together, finalise a first working draft, and write interface software, a workshop is organised at Brookhaven National Laboratory on the 20th-22nd October. The first day is intended to be a general open discussion day, whilst the others are intended to be "working" sessions where detailed specifications and code will be written. It would clearly be appropriate if the SAS community was represented at least for the first day discussions. Best Regards, Andy Hammersley ------------------------------------------------------------------------------ "imageNCIF": An Initiative to Standardise Image Formats ------------------------------------------------------- A P Hammersley ESRF, BP 220, 38043 Grenoble Cedex, France. E-mail: hammersley@esrf.fr Introduction ------------ Data formats and in particular image formats are a problem ! Most scientists will know the problem of having find or write a conversion program, to convert a file in a particular format to a format which can be input to the analysis program which they want to use. Similarly application programmers will know the problem that however many formats they support, there will always be new detectors with new data formats which will be required. If a sufficiently versatile common format was widely adopted this "Babylon" of formats would at least be limited and maybe the number would eventually decrease. Initiatives to define such formats are not new, but for storage of large quantities of experimental data there has been no commonly adopted format to date. For the task of passing more limited quantities of processed, typically structural, data amongst the crystallographic community, a common standard format has been defined: "CIF" [1]. "CIF" stands for "Crystallographic Information File", and is an ASCII text based, flexible and extensible human readable archive file format. In March 1995 a computing workshop was organised at the Brookhaven National Laboratory concentrating on the use and design of "Graphical User Interfaces" (GUI's). One subject area which was clearly of general common interest was image formats. A working group was formed and time was dedicated to an open discussion on the requirements of such a format. It was here (to my knowledge) that the idea of extending the CIF-concept to define the header information for images was first discussed by a sizeable group. What is CIF ? ------------- CIF is a standard format maintained and ``owned'' by the International Union of Crystallography (IUCr) for archiving and transporting crystallographic data [1]. One important current use is the submission of papers on structure determinations to Acta Crystallographica Section C. The format consists of simple ASCII text keyword and keyword value pairs. A large "dictionary" defines the keywords and possible values. There is support for comments, for multi-line character text, and for structuring separate data sections. The keywords are defined from a hierarchical "class" (data name categories) and "sub-class" system. e.g. All keywords which start with _diffrn refer to data from diffraction or other experimental measurements. A typical line from a CIF file, which could also be relevant to an experimental image file is: _diffrn_radiation_wavelength 0.76 # This is 16.3 keV Importantly, the dictionary defines the precise meaning of the data names, and the units and valid range when appropriate. A number of software tools are available from the IUCr to work with CIF's, and libraries are available to help read and write CIF's. CIF is maintained and extended through the IUCr COMCIFS committee. At present there are initiatives to extend CIF (Core dictionary) to cover the extra needs of macromolecular crystallography (mmCIF) and powder diffraction. For more information on CIF, there is a World-Wide-Web page with links to associated pages (http://www.iucr.ac.uk/cif/home.html). What is "imageNCIF" ? "imageNCIF" ( = image (Not) CIF; cf. mmCIF), is an E-mail based working/discussion group working on the idea of extending the CIF concept to cover the storage of experimental data, and in particular 2-D "image" data. There are presently about 15 members of this group, which contains representatives from commercial detector manufacturers, programmers of data analysis software, members concerned with data acquisition at user facilities, and crystallographers from a variety of different scientific disciplines. The aim is to standardise the passing of image and associated crystallographic experimental data from: one institute to another; one make of computer system to another; and from one computer program (acquisition or analysis) to another. It is desirable that image file contains the necessary associated experimental information to make data processing as automatic as possible. The basic aim is essentially the same as that of CIF, but the difference in the quantities of data involved mean that there is agreement amongst the members of the group that the ASCII encoding of image data is not appropriate. Given that it is highly desirable that header information and the image data are kept together in the same file this means that the format is binary in nature, and cannot be considered as compliant CIF. Hence the "Not" in "imageNCIF". Nevertheless, the advantage of using the existing CIF structure for naming and defining data names and definition is sufficiently important to define an associated format which is closely related to CIF: "CIF-compatible". The header section of such a file would contain CIF keyword / value pairs. This would differ from CIF in the manner in which the "lines" were separated. A simple utility program could extract the header section and write it out in a true CIF form. Similarly analysis programs might use some of the header information for their own processing, ignore other items, and write an output CIF which contains their results plus most of the original CIF-style items. A number of new CIF data names need to be defined. The details of this approach are presently being discussed by the working group. Joining "imageNCIF" So far there are no "rules" and "imageNCIF" seems to work reasonably well on an open membership basis. I suggest that one representative per institute, or one per scientific group within an institute is a sensible manner in which to channel views whilst avoiding that the working group gets too big. Input from the SAS community would be valuable, either through individuals or through a representative member. 1. S R Hall, F H Allen, I D Brown, Acta Cryst., A47, pp655-685, (1991)
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